- Home
- Bioconductor 3.1
- Software Packages
- PathNet
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")
In most cases, you don't need to download the package archive at all.
PathNet
|
|
|
|
|
|
|
An R package for pathway analysis using topological information
Bioconductor version: Release (3.1)
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
Author: Bhaskar Dutta <bhaskar.dutta at gmail.com>, Anders Wallqvist <awallqvist at bhsai.org>, and Jaques Reifman <jreifman at bhsai.org>
Maintainer: Jason B. Smith <jsmith at bhsai.org>
Citation (from within R,
enter citation("PathNet")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PathNet")
| R Script | PathNet | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, KEGG, MultipleComparison, Network, NetworkEnrichment, Pathways, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 1.14.0) |
| Imports | |
| LinkingTo | |
| Suggests | PathNetData, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | EnrichmentBrowser |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PathNet_1.8.0.tar.gz |
| Windows Binary | PathNet_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | PathNet_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | PathNet_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PathNet/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/PathNet/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
